Regardless of modify mode or whether the target blocks are inside of an InnerBlocks, shift-select always immediately folds the component making it currently unusable within components.
This appears to be fully resolved.
This issue is still occurring with identical behaviour.
In addition, when testing these, I also found the following two issues:
When copying a WP block (e.g. List block) from within an InnerBlocks in the navigator, you are not able to paste it using Cmd/Ctrl+V, only dragging it out works. This may be specific to blocks that hold other blocks, or may be specific to non-Cwicly blocks, we haven’t had time to fully test.
When dragging a block out of an InnerBlocks onto the root level of a page, after it is dropped, any folded Div blocks on the same level automatically unfold. (We have enabled “Expand on Click” and “Expand all by default” in the navigator settings, we haven’t tested without these).